2MBR

MURB WILD TYPE, COMPLEX WITH ENOLPYRUVYL-UDP-N-ACETYLGLUCOSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.

Benson, T.E.Walsh, C.T.Hogle, J.M.

(1997) Biochemistry 36: 806-811

  • DOI: 10.1021/bi962221g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosam ...

    MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine were solved and refined at 1.8 A resolution. The single point mutation of residue 229 from serine to alanine eliminated a hydroxyl group which has previously been proposed to play a critical role as a proton donor during the second half-reaction of MurB, namely, reoxidation of FADH2 and reduction of the enolpyruvyl substrate. The mutation also resulted in the loss of the water molecule-hydrogen bonded to the serine hydroxyl in the wild-type structure changing the hydrogen-bonding network with in the active site. Comparison of the wild-type and S229A mutant structures confirms that the dramatic kinetic defect of an approximately 10(7)-fold decrease observed for the Ser 229 Ala mutant in the second half-reaction [Benson, T.E., Walsh, C.T., & Massey, V. (1997) Biochemistry 36, 796-805] is a direct result of the loss of the serine hydroxyl moiety rather than other nonspecific active-site changes or general structural defects.


    Related Citations: 
    • Overexpression, Purification, and Mechanistic Study of Udp-N-Acetylenolpyruvylglucosamine Reductase
      Benson, T.E.,Marquardt, J.L.,Marquardt, A.C.,Etzkorn, F.A.,Walsh, C.T.
      (1993) Biochemistry 32: 2024
    • An Enzyme-Substrate Complex Involved in Bacterial Cell Wall Biosynthesis
      Benson, T.E.,Filman, D.J.,Walsh, C.T.,Hogle, J.M.
      (1995) Nat.Struct.Mol.Biol. 2: 644
    • Crystallization and Preliminary X-Ray Crystallographic Studies of Udp-N-Acetyl Enolpyruvylglucosamine Reductase
      Benson, T.E.,Walsh, C.T.,Hogle, J.M.
      (1994) Int.Immunol. 3: 1125


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASE
A
340Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: murB (yijB)
EC: 1.3.1.98
Find proteins for P08373 (Escherichia coli (strain K12))
Go to UniProtKB:  P08373
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPU
Query on EPU

Download SDF File 
Download CCD File 
A
URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C20 H29 N3 O19 P2
BEGZZYPUNCJHKP-DBYWSUQTSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.300α = 90.00
b = 49.300β = 90.00
c = 262.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance